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- PDB-7c3l: Structure of L-lysine oxidase D212A/D315A in complex with L-tyrosine -

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Basic information

Entry
Database: PDB / ID: 7c3l
TitleStructure of L-lysine oxidase D212A/D315A in complex with L-tyrosine
ComponentsL-lysine oxidase
KeywordsOXIDOREDUCTASE / L-amino acid oxidase
Function / homology
Function and homology information


L-lysine oxidase / L-lysine oxidase activity / L-amino-acid oxidase activity / amino acid catabolic process / nucleotide binding
Similarity search - Function
Amine oxidase / Flavin containing amine oxidoreductase / FAD/NAD(P)-binding domain superfamily
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / TYROSINE / L-Lysine alpha-oxidase / L-lysine oxidase
Similarity search - Component
Biological speciesHypocrea rufa (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsKitagawa, M. / Matsumoto, Y. / Inagaki, K. / Imada, K.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)24560962 Japan
CitationJournal: Protein Sci. / Year: 2020
Title: Structural basis of strict substrate recognition of l-lysine alpha-oxidase from Trichoderma viride.
Authors: Kondo, H. / Kitagawa, M. / Matsumoto, Y. / Saito, M. / Amano, M. / Sugiyama, S. / Tamura, T. / Kusakabe, H. / Inagaki, K. / Imada, K.
History
DepositionMay 12, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 23, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 4, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: L-lysine oxidase
B: L-lysine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,06912
Polymers121,5752
Non-polymers2,49410
Water24,2661347
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9750 Å2
ΔGint-43 kcal/mol
Surface area36770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.090, 170.480, 120.440
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein L-lysine oxidase


Mass: 60787.598 Da / Num. of mol.: 2 / Mutation: D212A,D315A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hypocrea rufa (fungus) / Plasmid: pCold IV / Production host: Escherichia coli (E. coli) / Strain (production host): SoluBL21
References: UniProt: A0A0J9X1X3, UniProt: A0A0G4DCU0*PLUS, L-lysine oxidase

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Non-polymers , 5 types, 1357 molecules

#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-TYR / TYROSINE


Type: L-peptide linking / Mass: 181.189 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H11NO3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1347 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.47 Å3/Da / Density % sol: 50.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 1% (w/v) PEG400, 0.1 M Tris-HCl pH7.5, 2.1 M Ammonium Sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 14, 2018
RadiationMonochromator: Double-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→75.3 Å / Num. obs: 111001 / % possible obs: 99.8 % / Redundancy: 5.8 % / Biso Wilson estimate: 17.03 Å2 / Rmerge(I) obs: 0.088 / Net I/σ(I): 9.9
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.235 / Mean I/σ(I) obs: 5 / Num. unique obs: 5429 / % possible all: 99.7

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Processing

Software
NameVersionClassification
BSSdata collection
PHENIX1.15.2_3472refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3X0V

3x0v


Resolution: 1.8→69.58 Å / SU ML: 0.1711 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.8207
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1903 5556 5.02 %
Rwork0.1594 105046 -
obs0.161 110602 99.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.4 Å2
Refinement stepCycle: LAST / Resolution: 1.8→69.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8018 0 166 1347 9531
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00848466
X-RAY DIFFRACTIONf_angle_d1.137111524
X-RAY DIFFRACTIONf_chiral_restr0.0551210
X-RAY DIFFRACTIONf_plane_restr0.00771466
X-RAY DIFFRACTIONf_dihedral_angle_d15.5553032
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.820.24051890.2043446X-RAY DIFFRACTION99.75
1.82-1.840.21331480.18623505X-RAY DIFFRACTION99.51
1.84-1.860.21361800.1863463X-RAY DIFFRACTION99.64
1.86-1.890.23432020.19053496X-RAY DIFFRACTION99.73
1.89-1.910.24231730.19763484X-RAY DIFFRACTION98.44
1.91-1.940.27091680.20113385X-RAY DIFFRACTION98.04
1.94-1.970.2091780.17563474X-RAY DIFFRACTION99.59
1.97-20.19281830.16363488X-RAY DIFFRACTION99.65
2-2.030.22911660.16483504X-RAY DIFFRACTION99.54
2.03-2.060.20661840.16353477X-RAY DIFFRACTION99.59
2.06-2.10.20212090.16563458X-RAY DIFFRACTION99.76
2.1-2.130.2021800.16543489X-RAY DIFFRACTION99.78
2.13-2.180.20471890.16723483X-RAY DIFFRACTION99.38
2.18-2.220.1912210.16983446X-RAY DIFFRACTION99.51
2.22-2.270.23691750.18593421X-RAY DIFFRACTION96.82
2.27-2.320.20351720.1663480X-RAY DIFFRACTION99.43
2.32-2.380.21021710.1573492X-RAY DIFFRACTION99.46
2.38-2.440.18212010.15553491X-RAY DIFFRACTION99.35
2.44-2.510.18811930.16043486X-RAY DIFFRACTION99.59
2.51-2.60.18762110.15933484X-RAY DIFFRACTION99.92
2.6-2.690.19481890.15893507X-RAY DIFFRACTION99.95
2.69-2.80.19831860.16123554X-RAY DIFFRACTION99.95
2.8-2.920.19321940.16523479X-RAY DIFFRACTION99.86
2.92-3.080.18721890.16053528X-RAY DIFFRACTION100
3.08-3.270.20011890.16493550X-RAY DIFFRACTION99.95
3.27-3.520.19221990.15023542X-RAY DIFFRACTION99.95
3.52-3.880.14761770.14583550X-RAY DIFFRACTION99.36
3.88-4.440.14891710.12743571X-RAY DIFFRACTION99.65
4.44-5.590.14981960.13353588X-RAY DIFFRACTION99.71
5.59-69.580.18031730.15933725X-RAY DIFFRACTION98.88

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